format_input1
Determine features of organisms, clades, taxonomic units, genes
Usage
format_input [-h]
[--output_table
OUTPUT_TABLE]
[-f
c,r]
[-c
[1..n_feats]]
[-s
[1..n_feats]]
[-o
float]
[-u
[1..n_feats]]
[-m
f,s]
[-n
int]
[-biom_c
BIOM_CLASS]
[-biom_s
BIOM_SUBCLASS]
INPUT_FILE
OUTPUT_FILE
Overview
LEfSe formatting modules
Options
positional arguments:
- INPUT_FILE
-
the input file, feature hierarchical level can be specified with | or . and those symbols must not be present for other reasons in the input file.
- OUTPUT_FILE
-
the output file containing the data for LEfSe
optional arguments:
-
-h, --help -
show this help message and exit
-
--output_table OUTPUT_TABLE -
the formatted table in txt format
-
-f {c,r} -
set whether the features are on rows (default) or on columns
-
-c [1..n_feats] -
set which feature use as class (default 1)
-
-s [1..n_feats] -
set which feature use as subclass (default
-1meaning no subclass)
-
-o float -
set the normalization value (default
-1.0 meaning no normalization)
-
-u [1..n_feats] -
set which feature use as subject (default
-1meaning no subject)
-
-m {f,s} -
set the policy to adopt with missin values: f removes the features with missing values, s removes samples with missing values (default f)
-
-n int -
set the minimum cardinality of each subclass (subclasses with low cardinalities will be grouped together, if the cardinality is still low, no pairwise comparison will be performed with them)
-
-biom_c BIOM_CLASS -
For biom input files: Set which feature use as class
-
-biom_s BIOM_SUBCLASS -
For biom input files: set which feature use as subclass